20.1.0rc3
*fMRIPrep* 20.1.0 introduces a magnitude of new features and improvements.
Originally nominated to become the first LTS (long-term support) version of *fMRIPrep*, this release has been supercharged with many new features and bug-fixes.
To ensure long-term stability, we have postponed the LTS nomination to 20.2 to allow us unlocking the 20.1 earlier, and a more extensive stress testing of the series before jumping into a longer support commitment.
Some key additions in this release include:
- A centralized `configuration module
<https://fmriprep.readthedocs.io/en/latest/api.html#module-fmriprep.config>`__
keeping track of *fMRIPrep*'s many options and run-time and environmental
circumstances and settings.
The new config module, which has been also propagated to other *NiPreps*
(`dMRIPrep <https://nipreps.org/dmriprep>`__,
`MRIQC <https://mriqc.readthedocs.io/>`__),
comes to robustify the run-to-run replicability of *fMRIPrep* (e.g., tracking random seeds),
make the option handling more modular but consistent (e.g., setting the ground for a
command-line interface built off of the config module),
and ease troubleshooting and telemetry.
- The *anatomical preprocessing fast-track*: a new command-line option
``--anat-derivatives <PATH>`` checks that all necessary anatomical derivatives
required by *fMRIPrep* are present under ``<PATH>``, and skips the anatomical
processing in full if *fMRIPrep*'s expectations are met.
Because now functional processing of many sessions and runs can be efficiently
split into more digestible computational units (i.e., cluster job) while guaranteeing the
exact same anatomical results are being used, this can significantly speed up
longitudinal study preprocessing, and it is a fundamental optimization to process
databases of densely scanned individuals such as `My Connectome
<https://openneuro.org/datasets/ds000031>`__.
- A change in output CIFTI2 subcortical volume orientation to be compatible with HCP Pipeline tools and data.
.. admonition:: Thanks
With thanks to Basile Pinsard, Joe B. Wexler, Noah Benson, and Marc Bue for contributions.
.. admonition:: New Paper!
This release comes after our latest protocol paper "*Analysis of task-based
functional MRI data preprocessed with fMRIPrep*" has been accepted.
The protocol describes how to use *fMRIPrep* on high-performance
clusters to preprocess fMRI data for task-based analyses.
Please check out `the latest version on Nature Protocols
<https://doi.org/10.1038/s41596-020-0327-3>`__ or `the preprint
<https://doi.org/10.1101/694364>`__.
.. caution::
As with all minor version increments, working directories
from previous versions **should not be reused**.
Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!
A full list of changes can be found below.
* FIX: Temporary config file in work directory gets clobbered in parallel jobs (#2138)
* FIX: Dismiss ``echo`` entity on several derivatives and figures outputs (#2133)
* FIX: Correct summary report when using previously run ``recon-all`` (#2124)
* FIX: Ensure correct WM and CSF masks are picked in confounds workflow (#2128)
* FIX: Explicitly add default ``native`` resolution to volumetric outputs (`nipreps/niworkflows#494`_)
* ENH: Finish the upstreaming of *NiTransforms* interfaces to *NiWorkflows* (#2132)
* ENH: Enable filtering for ``ANY`` or ``NONE`` in ``--bids-filter-file`` (#2123)
* ENH: Use new ``DerivativesDataSink`` from *NiWorkflows* 1.2.0 (#2114)
* ENH: Config module (#2018)
* ENH: Add option to ignore T2w / FLAIR images (#2015)
* ENH: Ensure subcortical volume in CIFTI is in LAS orientation (`nipreps/niworkflows#484`_)
* ENH: Add option to skip brain extraction (#2039)
* ENH: Use CIFTI sampling for carpetplot when available (#2055)
* MAINT: Stop printing full boilerplate, ``black fmriprep/cli`` (#2119)
* MAINT: Ensure YAML loader is specified (#2125)
* MAINT: PIN *tedana* version (#2117)
* MAINT: Bump minimum Python to 3.7 (#2017)
* MAINT: Remove unused console scripts (#2048)
* MAINT: Reduce the overall size of outputs (`nipreps/niworkflows#492`_)
* DOC: Update parallel subject neurostars link in FAQ (#2104)
* DOC: Add FAQ about reusing work directory (#2045)
.. _`nipreps/niworkflows#484`: https://github.com/nipreps/niworkflows/pull/484
.. _`nipreps/niworkflows#494`: https://github.com/nipreps/niworkflows/pull/494
.. _`nipreps/niworkflows#492`: https://github.com/nipreps/niworkflows/pull/492